Sequences are sent to a category (Pink, Red, Orange, Yellow, Grey) according to their mutation profile. FluWarnSystem counts the amount of mutations in 3 categories:
MOC - Mutation of Concern
Those are mutations that have been identified previously in the literature as changing the potential of the virus. The table of all MOC with their bibliographical reference is at the bottom in the MOC table.
ROI - Region of Interest
Those are important regions of the gene like for example Antigenic sites or Receptor-binding sites. The table of all ROI with their bibliographical reference is at the bottom in the ROI table.
PM - Private Mutation
Mutations that are neither a MOC nor a ROI.
The report was generated for the following input fasta file:
## > gisaid_epiflu_sequence.fasta
The sequences are from the subtype:
## > Influenza A H1N1pdm
Sequences that are not aligned were skipped because they were thrown out by Nextclade due to errors. For more information, please check the table in the section Skipped Sequences in the QC Report.
## > Sequences total in fasta file: 809
## > Sequences aligned: 802
## > Sequences skipped: 7
## > Metadata was given for the following amount of sequences: 813
## > Sequences in Group PINK: 98
## > Sequences in Group RED: 0
## No sequences in Group RED
## No sequences in Group RED
## No sequences in Group RED
## > Sequences in Group ORANGE: 2
## > Sequences in Group YELLOW: 1
## > Sequences in Group GREY: 701
The results from this report were calculated with the following reference sequence:
## The Influenza A H1N1pdm reference sequence A/Wisconsin/588/2019 MW626065 was used.
The annotations are generated with Nextclade. The following references are supported for the different Influenza subtypes.
The following table shows a list of the Mutations of Concern that were used to generate the Report.
The following table shows a list of Regions of Interest that were used to generate the Report.
The following table shows the fixed mutations for the season, which were excluded from the scoring.